Ishmael is a new character in Metal Gear Solid V: The Phantom Pain. He initially reveals himself several weeks after Big Boss awakens in the Cypriot hospital when the mysterious group infiltrates the hospital in order to kill Big Boss. Ishmael introduces himself and, when asked who he is, responds "You're talking to yourself. Been watching over you for 9 years." His true identity remains unknown until the game's end.

Ishmael's name comes from the main character from the classic novel Moby Dick. He refers to Big Boss as Ahab, a reference to Captain Ahab in the same novel.

Ishmael was a large part of the initial marketing campaign for The Phantom Pain. When the game was first revealed at the 2012 Spike Video Game Awards simply as its subtitle, without the key title of Metal Gear Solid V, Ishmael was a key character in the reveal trailer. During an interview with the supposed director at the appropriately named Moby Dick Studios, the man wore bandages on his face to look exactly like Ishmael. Later, at GDC 2013, Hideo Kojima removed an Ishmael mask to reveal the game officially as Metal Gear Solid V: The Phantom Pain.

On March 11, 1984, Ishmael saved Venom Snake from being assassinated by Quiet, and managed to fight her off by throwing bottles of various medical substance at her, which eventually engulfed her in flames and caused her to jump out of the window to escape. He then assisted Snake out of the hospital and to safety.

Ishmael claimed that he was a former acquaintance of Venom Snake and had been watching over him for the last 9 years while he was in a coma following XOF's attack on Mother Base. After giving Snake a shot of digoxin that helped him to move somewhat and escorted Snake to the stairs before deciding to take the elevator after realizing he wasn't recovered enough to actually walk. They eventually arrive at the elevators, but encounter a child wearing a gas mask standing in their path, who levitated through the ceiling.

Directly after this, the elevator doors explode, setting Ishmael on fire as an demonic apparition, later known as the Man on Fire, appears before disappearing due to the activation of the emergency sprinklers. Ishmael then led Venom Snake back the way they had come, in the flame-covered room, towards the emergency stairs. He proceeded to hijack an ambulance and drove Venom Snake to safety, although he disappeared in the car crash after Ocelot had arrived to rescue Venom.

In the secret ending, it is revealed that Ishmael is the first to awake from the car crash, being pulled from the vehicle by Ocelot himself. Ishmael, who is now known to be the real Big Boss, removes his bandages and is given clothing, an eyepatch and a bike so he can leave the scene. Ocelot tells Big Boss that the "double" (Venom Snake) will be fine with the title and already believes himself to be Big Boss. For all intents and purposes, Venom Snake is the "Big Boss" now.

Later, Ishmael/Big Boss sends a tape to Venom Snake telling Venom that he (Ishmael) is the actual Big Boss, but tells Venom that he is also Big Boss as he has carved out his own future. He says the two have created "legends" and the Venom Snake is considered a "friend" as he now holds he title in Diamond Dogs.

The opposite side of the tape reads "Operation Intrude N313" and Venom Snake puts it into an MSX bitcorder, implying that Big Boss is warning Venom of Solid Snake's arrival at Outer Heaven.